I used to speculate that Kotal Kahn is an ancestor of Shao Kahn, making him a demi-god.
Well, if he is truly the War, Sun and Blood god, probally one of this things was missing, and I doubt is sun lol.
Maybe he is powered by sacrifice and chaos, and without Kahn we lost a big part of it. Who knows if he does not ally himself with a major villain to see the world burn.
Also, if he is son of Shao Kahn, that makes more impossible form him to be a god, unless the Konqueror is a god, but this would elevate the level of plot twist to a not very interesting way.
I can't see a Shao Kahn's son/daughter being more powerful than him, except if Shao Kahn is the descendant of a full god.